Bhanapot was chairman of Thaksin's media empire, Shin Corp, at the time of the deal in 1997.
Thaksin transferred shares in Shin Corp to relatives and associates, including one of his maids, Duangta Wongpaki, before taking public office.
Investigators say Thaksin's wife, Pojaman, subsequently bought the shares from Duangta and transferred them to her brother, calling the "a gift" to avoid tax.
The anti-graft agency says Pojaman and Bhanapot engaged in illegal activity to avoid paying taxes and ruled the deal a handout.
In a separate case, Thailand's revenue department ruled that Thaksin's son and daughter would have to pay taxes on the family's sale of Shin Corp earlier this year to Temasek Holdings, the Singapore government's investment arm.
Drugs war probe
Last week, the Thai government ordered investigations into alleged abuses during Thaksin's "war on drugs" campaign.
About 2,500 people were killed during the campaign which started in 2003. Thaksin's government said the deaths were largely the result of drug dealers killing each other.
But rights groups say they were mostly due to extra-judicial killings by police.
Thailand was inundated with methamphetamine from neighbouring Myanmar at the time the campaign kicked off. It initially succeeded in cutting off supply, but anti-drug agencies say business soon returned to normal levels.
Thailand's military leadership has come under criticism in recent weeks for not being aggressive or decisive enough in fighting and investigating graft.
It has also come under fire for giving top government posts to soldiers.
The interim government used Thaksin's "high crimes" as justification for the coup and has promised to make curbing corruption a top priority.